Other methods have been discussed. For example, mods could be crippled. DBM didn't exist back then, and the other boss that did that I don't remember the name of, didn't do as much back then as DBM does now. If our goal is to recreate the experience as it was, then obviously not having DBM would be a reasonable way to accomplish that. DBM simply existing, makes the game today easier than it was. So disallow it. Again, this is completely consistent with the spirit of vanilla. Remember one-button-decursing? That was nerfed. They crippled the capabilities of the modding API to disallow that because it made the game too easy. So what if they cripple it a little bit more to once again make the game less easy?
If your pet's health gets too low or its attacks aren't very effective against a certain combatant, you can always switch out your current pet with another companion on your team. Only pets that are considered active (i.e., those in your three Battle Pet Slots), may be switched in and out during the battle. Once the match is over, you can always change up your active pet team, which is useful if one of your pets is low on health or dead.
Bonz has the upper hand, as his Zombie-Type monsters gain a 30% ATK and DEF bonus because of the Graveyard Field, and when they are destroyed, they just regenerate, and become even stronger from "Call of the Haunted". However, when Yugi and the gang arrive, Joey manages to figure out the Zombie's main weakness and that is their DEF is 0. Using "Shield & Sword" to switch their ATK and DEF values, Joey wins the Duel. Bandit Keith then locks the gang in, double crosses his three companions, and enters the Duelist Kingdom Finals after taking Zygor and Sid's five Star Chips by force.
Occasionally it's also been proposed to re-randomize all the gear. We didn't have best in slot lists back then. People weren't starting out as a fresh level 1 character with a complete list of which dungeons to run at 60 in order to gear as quickly and efficiently as possible. Now, all that data is available. If gear were re-randomized then all of those lists would become useless and thing would be close to how they were. Which is a more important part of the "vanilla experience?" the fact that item X from boss Y has exactly Z stats on it, or the voyage of discovery? Personally I think that voyage is way more important. Do you remember how many points of which stat on the ring or whatever that Darkmaster Gandling drops? I don't. Would it kill your experience if the BiS for every class were in a different dungeon so people had to actually play to figure it out rather than simply consult a spreadsheet? I don't think it would. For that matter, it probably wouldn't be a bad idea to handle it intelligently so that the better gear is in later dungeons. I remember there because some weird cases where level 40ish gear was better than anything that dropped in level 60 dungeons.